Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 85L4Y

Calculation Name: 5DDT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DDT

Chain ID: A

ChEMBL ID:

UniProt ID: Q06755

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2825787.013459
FMO2-HF: Nuclear repulsion 2735423.182553
FMO2-HF: Total energy -90363.830906
FMO2-MP2: Total energy -90628.789452


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-19.559-19.04611.917-5.583-6.845-0.044
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.031
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3TYR0-0.027-0.0533.438-0.8800.1060.019-0.163-0.8420.002
4A4ASP-1-0.796-0.8716.563-0.892-0.8920.0000.0000.0000.000
5A5VAL0-0.008-0.0189.722-0.028-0.0280.0000.0000.0000.000
6A6VAL0-0.0150.00012.4680.0790.0790.0000.0000.0000.000
7A7ILE00.0160.00415.7330.0270.0270.0000.0000.0000.000
8A8PRO0-0.051-0.01218.4900.0240.0240.0000.0000.0000.000
9A9ALA00.0600.01121.6720.0190.0190.0000.0000.0000.000
10A10ALA0-0.029-0.00824.9220.0190.0190.0000.0000.0000.000
11A11GLY00.0350.01125.031-0.013-0.0130.0000.0000.0000.000
12A12GLN0-0.026-0.00422.8230.0120.0120.0000.0000.0000.000
13A13GLY00.0760.03127.0350.0110.0110.0000.0000.0000.000
14A14LYS10.9000.96030.7450.0750.0750.0000.0000.0000.000
15A15ARG10.9720.99131.6030.1380.1380.0000.0000.0000.000
16A16MET0-0.0260.00034.5780.0100.0100.0000.0000.0000.000
17A17LYS10.9450.96936.1180.0630.0630.0000.0000.0000.000
18A18ALA00.0630.02635.721-0.001-0.0010.0000.0000.0000.000
19A19GLY00.0300.00034.5620.0080.0080.0000.0000.0000.000
20A20ARG10.8300.90435.4780.0760.0760.0000.0000.0000.000
21A21ASN0-0.0070.00529.2870.0030.0030.0000.0000.0000.000
22A22LYS10.9380.96130.8640.0930.0930.0000.0000.0000.000
23A23LEU00.0350.01825.0130.0040.0040.0000.0000.0000.000
24A24PHE0-0.036-0.02128.3260.0010.0010.0000.0000.0000.000
25A25ILE0-0.049-0.01230.9020.0080.0080.0000.0000.0000.000
26A26GLU-1-0.916-0.94530.650-0.048-0.0480.0000.0000.0000.000
27A27LEU00.0020.00227.0130.0020.0020.0000.0000.0000.000
28A28LYS10.8360.89129.7140.0200.0200.0000.0000.0000.000
29A29GLY00.0190.01931.1120.0040.0040.0000.0000.0000.000
30A30ASP-1-0.749-0.84627.473-0.036-0.0360.0000.0000.0000.000
31A31PRO0-0.009-0.00327.759-0.004-0.0040.0000.0000.0000.000
32A32VAL0-0.011-0.00625.416-0.003-0.0030.0000.0000.0000.000
33A33ILE0-0.014-0.00821.982-0.006-0.0060.0000.0000.0000.000
34A34ILE00.0180.01622.569-0.018-0.0180.0000.0000.0000.000
35A35HIS0-0.017-0.01722.0860.0000.0000.0000.0000.0000.000
36A36THR0-0.028-0.03418.8710.0070.0070.0000.0000.0000.000
37A37LEU0-0.031-0.00818.087-0.022-0.0220.0000.0000.0000.000
38A38ARG10.8850.93917.1960.0290.0290.0000.0000.0000.000
39A39VAL0-0.0120.02814.1770.0190.0190.0000.0000.0000.000
40A40PHE00.020-0.01611.8860.0200.0200.0000.0000.0000.000
41A41ASP-1-0.801-0.87712.445-0.129-0.1290.0000.0000.0000.000
42A42SER0-0.044-0.02313.6170.0400.0400.0000.0000.0000.000
43A43HIS0-0.0030.0477.380-0.181-0.1810.0000.0000.0000.000
44A44ARG10.9670.9645.937-1.394-1.3940.0000.0000.0000.000
45A45GLN0-0.020-0.0113.430-0.5120.0420.023-0.125-0.4520.000
46A46CYS0-0.0040.0245.633-0.948-0.9480.0000.0000.0000.000
47A47ASP-1-0.778-0.8545.147-2.138-2.098-0.001-0.004-0.0350.000
48A48LYS10.8040.9078.2450.9010.9010.0000.0000.0000.000
49A49ILE00.0240.01411.557-0.111-0.1110.0000.0000.0000.000
50A50ILE0-0.040-0.00214.0140.0560.0560.0000.0000.0000.000
51A51LEU00.0240.01316.742-0.003-0.0030.0000.0000.0000.000
52A52VAL0-0.042-0.01920.1640.0200.0200.0000.0000.0000.000
53A53ILE00.0100.00922.6710.0160.0160.0000.0000.0000.000
54A54ASN00.0530.02726.2290.0030.0030.0000.0000.0000.000
55A55GLU-1-0.793-0.90229.775-0.153-0.1530.0000.0000.0000.000
56A56GLN0-0.039-0.03131.0160.0050.0050.0000.0000.0000.000
57A57GLU-1-0.821-0.91230.694-0.116-0.1160.0000.0000.0000.000
58A58ARG10.8480.92625.2110.1740.1740.0000.0000.0000.000
59A59GLU-1-0.884-0.93729.303-0.094-0.0940.0000.0000.0000.000
60A60HIS00.0200.00431.3650.0000.0000.0000.0000.0000.000
61A61PHE00.0060.00025.4480.0010.0010.0000.0000.0000.000
62A62GLN00.005-0.00826.797-0.002-0.0020.0000.0000.0000.000
63A63GLN0-0.052-0.00827.8630.0020.0020.0000.0000.0000.000
64A64LEU00.007-0.00326.8120.0050.0050.0000.0000.0000.000
65A65LEU0-0.021-0.03622.1530.0010.0010.0000.0000.0000.000
66A66SER0-0.097-0.03525.0670.0060.0060.0000.0000.0000.000
67A67ASP-1-0.888-0.94227.549-0.048-0.0480.0000.0000.0000.000
68A68TYR0-0.086-0.04224.2620.0090.0090.0000.0000.0000.000
69A69PRO0-0.0290.01022.959-0.010-0.0100.0000.0000.0000.000
70A70PHE0-0.018-0.03318.056-0.006-0.0060.0000.0000.0000.000
71A71GLN0-0.093-0.04714.1600.0510.0510.0000.0000.0000.000
72A72THR00.001-0.02012.0510.0050.0050.0000.0000.0000.000
73A73SER0-0.044-0.01413.2870.0170.0170.0000.0000.0000.000
74A74ILE00.0530.01614.694-0.070-0.0700.0000.0000.0000.000
75A75GLU-1-0.939-0.97016.999-0.383-0.3830.0000.0000.0000.000
76A76LEU0-0.011-0.00218.764-0.016-0.0160.0000.0000.0000.000
77A77VAL00.0050.00119.8090.0120.0120.0000.0000.0000.000
78A78ALA0-0.0040.01322.8490.0050.0050.0000.0000.0000.000
79A79GLY00.018-0.01125.864-0.020-0.0200.0000.0000.0000.000
80A80GLY0-0.0080.00626.6010.0190.0190.0000.0000.0000.000
81A81ASP-1-0.902-0.97428.508-0.151-0.1510.0000.0000.0000.000
82A82GLU-1-0.920-0.96128.491-0.170-0.1700.0000.0000.0000.000
83A83ARG10.9090.94619.8080.2940.2940.0000.0000.0000.000
84A84GLN00.0760.04523.181-0.012-0.0120.0000.0000.0000.000
85A85HIS00.0350.00723.101-0.025-0.0250.0000.0000.0000.000
86A86SER0-0.014-0.01323.981-0.014-0.0140.0000.0000.0000.000
87A87VAL00.0220.00918.045-0.017-0.0170.0000.0000.0000.000
88A88TYR00.0140.01619.357-0.038-0.0380.0000.0000.0000.000
89A89LYS10.8460.91020.5110.2390.2390.0000.0000.0000.000
90A90GLY00.0280.00419.123-0.005-0.0050.0000.0000.0000.000
91A91LEU00.0290.00914.618-0.050-0.0500.0000.0000.0000.000
92A92LYS10.8760.94216.3300.2820.2820.0000.0000.0000.000
93A93ALA0-0.0110.01417.1190.0190.0190.0000.0000.0000.000
94A94VAL0-0.036-0.00111.041-0.007-0.0070.0000.0000.0000.000
95A95LYS10.9290.95911.9450.4710.4710.0000.0000.0000.000
96A96GLN0-0.034-0.0207.3530.2250.2250.0000.0000.0000.000
97A97GLU-1-0.782-0.8709.095-1.368-1.3680.0000.0000.0000.000
98A98LYS10.7710.8715.5892.0542.0540.0000.0000.0000.000
99A99ILE00.0400.0303.9000.3810.5970.000-0.024-0.1910.000
100A100VAL0-0.026-0.0096.334-0.023-0.0230.0000.0000.0000.000
101A101LEU00.0190.0027.7970.1290.1290.0000.0000.0000.000
102A102VAL0-0.024-0.00110.9930.0250.0250.0000.0000.0000.000
103A103HIS00.0640.00514.7410.0190.0190.0000.0000.0000.000
104A104ASP-1-0.805-0.90616.629-0.231-0.2310.0000.0000.0000.000
105A105GLY00.0510.01320.2830.0100.0100.0000.0000.0000.000
106A106ALA0-0.015-0.00621.7910.0180.0180.0000.0000.0000.000
107A107ARG10.8330.92720.1210.1840.1840.0000.0000.0000.000
108A108PRO00.0590.04120.102-0.014-0.0140.0000.0000.0000.000
109A109PHE00.0040.01020.5270.0080.0080.0000.0000.0000.000
110A110ILE0-0.0320.00514.3420.0190.0190.0000.0000.0000.000
111A111LYS10.8850.94315.6810.0060.0060.0000.0000.0000.000
112A112HIS00.008-0.02011.0990.0320.0320.0000.0000.0000.000
113A113GLU-1-0.892-0.93610.5610.2360.2360.0000.0000.0000.000
114A114GLN00.0440.01211.3820.0370.0370.0000.0000.0000.000
115A115ILE0-0.029-0.0048.207-0.037-0.0370.0000.0000.0000.000
116A116ASP-1-0.864-0.9366.8970.7450.7450.0000.0000.0000.000
117A117GLU-1-0.956-0.9877.2100.3880.3880.0000.0000.0000.000
118A118LEU0-0.055-0.0299.373-0.113-0.1130.0000.0000.0000.000
119A119ILE0-0.011-0.0062.949-1.621-0.7700.475-0.494-0.8320.004
120A120ALA00.0200.0245.276-0.650-0.6500.0000.0000.0000.000
121A121GLU-1-0.809-0.9206.234-0.842-0.8420.0000.0000.0000.000
122A122ALA0-0.0070.0017.073-0.123-0.1230.0000.0000.0000.000
123A123GLU-1-0.916-0.9681.964-15.333-17.46711.401-4.773-4.493-0.050
124A124GLN0-0.051-0.0076.3640.0950.0950.0000.0000.0000.000
125A125THR0-0.078-0.0589.3260.0470.0470.0000.0000.0000.000
126A126GLY0-0.033-0.00310.4000.0770.0770.0000.0000.0000.000
127A127ALA00.022-0.01011.458-0.082-0.0820.0000.0000.0000.000
128A128ALA0-0.0070.01810.9260.0780.0780.0000.0000.0000.000
129A129ILE00.0170.00612.807-0.035-0.0350.0000.0000.0000.000
130A130LEU00.0490.03114.6210.0370.0370.0000.0000.0000.000
131A131ALA0-0.029-0.01416.637-0.014-0.0140.0000.0000.0000.000
132A132VAL0-0.0110.01320.3050.0180.0180.0000.0000.0000.000
133A133PRO00.0700.05523.299-0.010-0.0100.0000.0000.0000.000
134A134VAL00.0090.02126.4510.0060.0060.0000.0000.0000.000
135A135LYS10.9300.96129.3520.0420.0420.0000.0000.0000.000
136A136ASP-1-0.876-0.92632.336-0.053-0.0530.0000.0000.0000.000
137A137THR0-0.098-0.07534.409-0.004-0.0040.0000.0000.0000.000
138A138ILE00.0620.05032.569-0.001-0.0010.0000.0000.0000.000
139A139LYS10.9050.93935.9760.0600.0600.0000.0000.0000.000
140A140ARG10.9350.99034.3540.0980.0980.0000.0000.0000.000
141A141VAL0-0.027-0.02239.1550.0050.0050.0000.0000.0000.000
142A142GLN00.0130.00540.690-0.005-0.0050.0000.0000.0000.000
143A143ASP-1-0.898-0.94144.383-0.063-0.0630.0000.0000.0000.000
144A144LEU0-0.054-0.04144.3560.0030.0030.0000.0000.0000.000
145A145GLN00.0460.03746.3310.0030.0030.0000.0000.0000.000
146A146VAL0-0.065-0.04343.071-0.003-0.0030.0000.0000.0000.000
147A147SER0-0.020-0.00442.3150.0010.0010.0000.0000.0000.000
148A148GLU-1-0.858-0.93439.057-0.085-0.0850.0000.0000.0000.000
149A149THR0-0.049-0.03039.0230.0000.0000.0000.0000.0000.000
150A150ILE0-0.0040.00233.2100.0000.0000.0000.0000.0000.000
151A151GLU-1-0.875-0.94434.217-0.072-0.0720.0000.0000.0000.000
152A152ARG10.9840.97832.9410.0510.0510.0000.0000.0000.000
153A153SER0-0.089-0.03331.653-0.003-0.0030.0000.0000.0000.000
154A154SER00.0380.01628.3590.0010.0010.0000.0000.0000.000
155A155LEU0-0.0230.00327.354-0.011-0.0110.0000.0000.0000.000
156A156TRP00.016-0.00321.4610.0070.0070.0000.0000.0000.000
157A157ALA0-0.043-0.02325.330-0.009-0.0090.0000.0000.0000.000
158A158VAL00.0180.01119.7950.0070.0070.0000.0000.0000.000
159A159GLN0-0.061-0.04119.1500.0100.0100.0000.0000.0000.000
160A160THR0-0.040-0.01016.828-0.019-0.0190.0000.0000.0000.000
161A161PRO00.0510.00312.5020.0360.0360.0000.0000.0000.000
162A162GLN0-0.059-0.04213.7420.0190.0190.0000.0000.0000.000
163A163ALA00.0120.0158.285-0.068-0.0680.0000.0000.0000.000
164A164PHE00.0490.0069.7500.0900.0900.0000.0000.0000.000
165A165ARG10.9010.9648.5520.9200.9200.0000.0000.0000.000
166A166LEU00.0030.0019.7460.2620.2620.0000.0000.0000.000
167A167SER0-0.062-0.06311.8840.2170.2170.0000.0000.0000.000
168A168LEU0-0.033-0.00613.4290.1180.1180.0000.0000.0000.000
169A169LEU00.0460.03314.0280.0970.0970.0000.0000.0000.000
170A170MET00.000-0.00415.7200.0990.0990.0000.0000.0000.000
171A171LYS10.9180.97017.7630.4460.4460.0000.0000.0000.000
172A172ALA00.0560.02518.7710.0480.0480.0000.0000.0000.000
173A173HIS00.012-0.02318.4350.0670.0670.0000.0000.0000.000
174A174ALA0-0.061-0.01421.6020.0370.0370.0000.0000.0000.000
175A175GLU-1-0.962-0.99523.349-0.265-0.2650.0000.0000.0000.000
176A176ALA0-0.024-0.00824.3340.0280.0280.0000.0000.0000.000
177A177GLU-1-0.928-0.97425.678-0.239-0.2390.0000.0000.0000.000
178A178ARG10.9010.95727.5910.2360.2360.0000.0000.0000.000
179A179LYS10.8990.94927.2040.2430.2430.0000.0000.0000.000
180A180GLY0-0.0060.00730.6780.0120.0120.0000.0000.0000.000
181A181PHE0-0.053-0.02125.6160.0090.0090.0000.0000.0000.000
182A182LEU0-0.002-0.01227.822-0.014-0.0140.0000.0000.0000.000
183A183GLY00.0490.03325.2200.0110.0110.0000.0000.0000.000
184A184THR0-0.079-0.05225.665-0.006-0.0060.0000.0000.0000.000
185A185ASP-1-0.800-0.88820.494-0.270-0.2700.0000.0000.0000.000
186A186ASP-1-0.792-0.88217.223-0.416-0.4160.0000.0000.0000.000
187A187ALA00.0380.02517.727-0.018-0.0180.0000.0000.0000.000
188A188SER00.013-0.00618.7320.0040.0040.0000.0000.0000.000
189A189LEU0-0.049-0.03620.3700.0170.0170.0000.0000.0000.000
190A190VAL0-0.024-0.02216.221-0.006-0.0060.0000.0000.0000.000
191A191GLU-1-0.936-0.98119.603-0.250-0.2500.0000.0000.0000.000
192A192GLN0-0.041-0.00222.1860.0180.0180.0000.0000.0000.000
193A193MET0-0.106-0.02718.4300.0070.0070.0000.0000.0000.000
194A194GLU-1-0.933-0.97123.754-0.196-0.1960.0000.0000.0000.000
195A195GLY0-0.045-0.02423.186-0.017-0.0170.0000.0000.0000.000
196A196GLY0-0.0320.00619.675-0.029-0.0290.0000.0000.0000.000
197A197SER0-0.066-0.04518.1200.0300.0300.0000.0000.0000.000
198A198VAL00.0280.01015.988-0.057-0.0570.0000.0000.0000.000
199A199ARG10.8590.94514.1700.2850.2850.0000.0000.0000.000
200A200VAL0-0.006-0.00415.549-0.023-0.0230.0000.0000.0000.000
201A201VAL00.0030.00512.4470.0090.0090.0000.0000.0000.000
202A202GLU-1-0.944-0.97415.851-0.053-0.0530.0000.0000.0000.000
203A203GLY00.0260.01017.9880.0200.0200.0000.0000.0000.000
204A204SER00.0110.00819.1500.0090.0090.0000.0000.0000.000
205A205TYR0-0.022-0.05221.874-0.012-0.0120.0000.0000.0000.000
206A206THR0-0.013-0.00923.331-0.002-0.0020.0000.0000.0000.000
207A207ASN0-0.028-0.00318.522-0.001-0.0010.0000.0000.0000.000
208A208ILE00.003-0.01022.372-0.018-0.0180.0000.0000.0000.000
209A209LYS10.8510.92424.2900.1670.1670.0000.0000.0000.000
210A210LEU0-0.048-0.02925.6060.0080.0080.0000.0000.0000.000
211A211THR0-0.056-0.03828.319-0.007-0.0070.0000.0000.0000.000
212A212THR0-0.077-0.05030.8210.0040.0040.0000.0000.0000.000
213A213PRO00.007-0.02833.7890.0000.0000.0000.0000.0000.000
214A214ASP-1-0.837-0.90935.965-0.048-0.0480.0000.0000.0000.000
215A215ASP-1-0.812-0.90330.396-0.082-0.0820.0000.0000.0000.000
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